In the European Union (EU), copper concentration in agricultural soil stems from anthropogenic activities and natural sources (soil and geology). This manuscript reports a statistical comparison of copper concentrations at different levels of administrative units, with a focus on agricultural areas. Anthropogenic sources of diffuse copper contamination include fungicidal treatments, liquid manure (mainly from pigs), sewage sludge, atmospheric deposition, mining activities, local industrial contamination and particles from car brakes. Sales of fungicides in the EU are around 158,000 tonnes annually, a large proportion of which are copper based and used extensively in vineyards and orchards. Around 10 million tonnes of sewage sludge is treated annually in the EU, and 40% of this (which has a high copper content) is used as fertilizer in agriculture. In the EU, 150 million pigs consume more than 6.2 million tonnes of copper through additives in their feed, and most of their liquid manure ends up in agricultural soil. These three sources (sales of fungicides, sewage sludge and copper consumption for pigs feed) depend much on local traditional farming practices. Recent research towards replacing copper spraying in vineyards and policy developments on applying sewage and controlling the feed given to pigs are expected to reduce copper accumulation in agricultural soil.